Table 1.
Diffraction and refinement statistics
| Zn2+,Ca2+-S100B | Pnt-Ca2+-S100B | Pnt-Zn2+,Ca2+-S100B | |
|---|---|---|---|
| Diffraction statistics | |||
| Space group | C2221 | P41212 | P41212 |
| Cell dimensions: a, b, c (Å) | 34.6, 90.5, 58.3 | 63.6, 63.6, 48.2 | 62.9, 62.9, 50.1 |
| Cell angles: α, β, γ (°) | 90, 90, 90 | 90, 90, 90 | 90, 90, 90 |
| Resolution (Å) | 45.22–1.88 (1.93–1.88) | 44.95–2.15 (2.20–2.15) | 44.46–1.85 (1.90–1.85) |
| No. of unique reflections | 7120 (502) | 5502 (390) | 8456 (560) |
| Completeness (%) | 96.45 (91.90) | 99.98 (99.76) | 98.84 (93.20) |
| Rsyma | 0.056 (0.319) | 0.081 (0.667) | 0.150 (0.489) |
| Average I/σ | 23.4 (4.3) | 32.3 (4.2) | 20.4 (4.2) |
| Multiplicity | 6.6 (5.1) | 12 (12.1) | 12.9 (8.9) |
| Refinement statistics | |||
| Rcrysb(%) | 22.1 (31.1) | 21.1 (25.2) | 19.4 (21.2) |
| Rfreeb(%) | 26.8 (46.7) | 26.6 (26.7) | 24.3 (22.9) |
| Protein atoms | 727 | 729 | 737 |
| Water molecules | 51 | 35 | 82 |
| Non-hydrogen atoms | 768 | 814 | 858 |
| Mean B values (Å2) | |||
| Overall | 49.42 | 35.87 | 40.16 |
| Protein atoms | 50.19 | 35.05 | 39.01 |
| Water molecules | 51.34 | 35.59 | 45.94 |
| Ca2+ typical EF hand | 47.00 | 31.72 | 35.76 |
| Ca2+ S100B EF hand | 46.71 | 35.58 | 35.63 |
| Zn2+ | 50.11 | 43.17 | |
| Pnt site 1 | 53.14c | 49.85d | |
| Pnt site 2 | 43.01c | 67.52d | |
| RMSD | |||
| Bond length (Å) | 0.015 | 0.008 | 0.015 |
| Bond angles (Å) | 1.543 | 1.135 | 1.484 |
| Ramachandran plot (%)e | |||
| Most favored | 95.2 | 95.2 | 96.5 |
| Additionally allowed | 4.8 | 4.8 | 3.5 |
| PDB identification | 3CR2 | 3CR4 | 3CR5 |
Numbers in parentheses represent the last outer shell.
Rsym= ΣhklΣi(|Ihkl,i|-|〈Ihkl〉|)/ΣhklΣiIhkl,i, for a reflection hkl whose weighted mean over i observations is 〈I〉s.
Rcrys and Rfree = Σhkl||F o|-k|Fc||/Σhkl||Fo|, where |Fo| is the observed structure factor amplitude and |Fc| is the calculated structure factor amplitude for the working and test sets, respectively.
Mean B values (Å2) for Pnt in sites 1 and 2 are similar to the mean B value (38.74) for side-chain atoms of S100B involved in Pnt binding (Ile11, Asp12, His42, Cys84, Phe87, and Phe88).
Mean B values (Å2) for Pnt in sites 1 and 2 are similar to the mean B value (45.29) for side-chain atoms of S100B involved in the Pnt binding (Val8, Ile11, Phe43, Cys84, Phe87, and Phe88).
For Zn2+,Ca2+-S100B and Pnt-Ca2+-S100B, the calculations had 80 residues in the most favored region and 4 residues in additionally allowed regions. For Pnt-Zn2+,Ca2+-S100B, the calculations had 82 residues in the most favored region and 3 residues in additionally allowed regions.